"import caiman as cm" -> "import caiman"

bin/caiman_gui.py

@@ -12,7 +12,7 @@
 from pyqtgraph.parametertree import Parameter, ParameterTree
 from scipy.sparse import csc_matrix
 
-import caiman as cm
+import caiman
 from caiman.source_extraction.cnmf.cnmf import load_CNMF
 from caiman.source_extraction.cnmf.params import CNMFParams
 
@@ -67,10 +67,10 @@ def make_color_img(img, gain=255, min_max=None, out_type=np.uint8):
                                           directory=d, filter=f + ';;*.mmap')[0]
 
 if fpath[-3:] == 'nwb':
-    mov = cm.load(cnm_obj.mmap_file,
+    mov = caiman.load(cnm_obj.mmap_file,
                   var_name_hdf5='acquisition/TwoPhotonSeries')
 else:
-    mov = cm.load(cnm_obj.mmap_file)
+    mov = caiman.load(cnm_obj.mmap_file)
 
 estimates = cnm_obj.estimates
 params_obj = cnm_obj.params
@@ -106,7 +106,7 @@ def selectionchange(self,i):
     cb.show()
 
 if not hasattr(estimates, 'Cn'):
-    estimates.Cn = cm.local_correlations(mov, swap_dim=False)
+    estimates.Cn = caiman.local_correlations(mov, swap_dim=False)
 #Cn = estimates.Cn
 
 # We rotate our components 90 degrees right because of incompatibility of pyqtgraph and pyplot

caiman/behavior/behavior.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# -*- coding: utf-8 -*-
 
 """
 Functions related to optical flow
@@ -14,7 +13,7 @@
 from sklearn.decomposition import NMF
 import time
 
-import caiman as cm
+import caiman
 
 try:
     cv2.setNumThreads(0)
@@ -75,14 +74,14 @@ def extract_motor_components_OF(m,
         mask = coo_matrix(np.array(mask).squeeze())
         ms = [get_nonzero_subarray(mask.multiply(fr), mask) for fr in m]
         ms = np.dstack(ms)
-        ms = cm.movie(ms.transpose([2, 0, 1]))
+        ms = caiman.movie(ms.transpose([2, 0, 1]))
 
     else:
         ms = m
     of_or = compute_optical_flow(ms, do_show=False, polar_coord=False)
     of_or = np.concatenate([
-        cm.movie(of_or[0]).resize(resize_fact, resize_fact, 1)[np.newaxis, :, :, :],
-        cm.movie(of_or[1]).resize(resize_fact, resize_fact, 1)[np.newaxis, :, :, :]
+        caiman.movie(of_or[0]).resize(resize_fact, resize_fact, 1)[np.newaxis, :, :, :],
+        caiman.movie(of_or[1]).resize(resize_fact, resize_fact, 1)[np.newaxis, :, :, :]
     ],
                            axis=0)
 
@@ -130,8 +129,8 @@ def extract_magnitude_and_angle_from_OF(spatial_filter_,
             x, y = scipy.signal.medfilt(time_trace, kernel_size=[1, 1]).T
             x = scipy.signal.savgol_filter(x.squeeze(), sav_filter_size, 1)
             y = scipy.signal.savgol_filter(y.squeeze(), sav_filter_size, 1)
-            mag, dirct = to_polar(x - cm.components_evaluation.mode_robust(x),
-                                  y - cm.components_evaluation.mode_robust(y))
+            mag, dirct = to_polar(x - caiman.components_evaluation.mode_robust(x),
+                                  y - caiman.components_evaluation.mode_robust(y))
             dirct = scipy.signal.medfilt(dirct.squeeze(), kernel_size=1).T
 
         # normalize to pixel units
@@ -271,8 +270,8 @@ def compute_optical_flow(m,
 
     return mov_tot
 
+# NMF
 
-#%% NMF
 def extract_components(mov_tot,
                        n_components: int = 6,
                        normalize_std: bool = True,

caiman/mmapping.py

@@ -12,7 +12,7 @@
 from typing import Any, Optional, Union
 import pathlib
 
-import caiman as cm
+import caiman
 import caiman.paths
 
 def prepare_shape(mytuple:tuple) -> tuple:
@@ -412,7 +412,7 @@ def save_memmap(filenames:list[str],
 
             logging.debug('Distributing memory map over many files')
             # Here we make a bunch of memmap files in the right order. Same parameters
-            fname_parts = cm.save_memmap_each(filenames,
+            fname_parts = caiman.save_memmap_each(filenames,
                                               base_name=base_name,
                                               order=order,
                                               border_to_0=border_to_0,
@@ -432,7 +432,7 @@ def save_memmap(filenames:list[str],
         if order == 'F':
             raise Exception('You cannot merge files in F order, they must be in C order')
 
-        fname_new = cm.save_memmap_join(fname_parts, base_name=base_name,
+        fname_new = caiman.save_memmap_join(fname_parts, base_name=base_name,
                                         dview=dview, n_chunks=n_chunks)
 
     else:
@@ -458,9 +458,9 @@ def save_memmap(filenames:list[str],
 
             else:
                 if isinstance(f, (str, list)):
-                    Yr = cm.load(caiman.paths.fn_relocated(f), fr=1, in_memory=True, var_name_hdf5=var_name_hdf5)
+                    Yr = caiman.load(caiman.paths.fn_relocated(f), fr=1, in_memory=True, var_name_hdf5=var_name_hdf5)
                 else:
-                    Yr = cm.movie(f)
+                    Yr = caiman.movie(f)
                 if xy_shifts is not None:
                     Yr = Yr.apply_shifts(xy_shifts, interpolation='cubic', remove_blanks=False)
 
@@ -492,7 +492,7 @@ def save_memmap(filenames:list[str],
             fx, fy, fz = resize_fact
             if fx != 1 or fy != 1 or fz != 1:
                 if 'movie' not in str(type(Yr)):
-                    Yr = cm.movie(Yr, fr=1)
+                    Yr = caiman.movie(Yr, fr=1)
                 Yr = Yr.resize(fx=fx, fy=fy, fz=fz)
 
             T, dims = Yr.shape[0], Yr.shape[1:]
@@ -501,7 +501,7 @@ def save_memmap(filenames:list[str],
             Yr = np.ascontiguousarray(Yr, dtype=np.float32) + np.float32(0.0001) + np.float32(add_to_movie)
 
             if idx == 0:
-                fname_tot = cm.paths.generate_fname_tot(base_name, dims, order)
+                fname_tot = caiman.paths.generate_fname_tot(base_name, dims, order)
                 if isinstance(f, str):
                     fname_tot = caiman.paths.fn_relocated(os.path.join(os.path.split(f)[0], fname_tot))
                 if len(filenames) > 1:
@@ -643,7 +643,7 @@ def save_tif_to_mmap_online(movie_iterable, save_base_name='YrOL_', order='C', a
 
     if isinstance(movie_iterable, str):         # Allow specifying a filename rather than its data rep
         with tifffile.TiffFile(movie_iterable) as tf:  # And load it if that happens
-            movie_iterable = cm.movie(tf)
+            movie_iterable = caiman.movie(tf)
 
     count = 0
     new_mov = []